Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004958.1 Corchorus capsularis cultivar CVL-1 contig04976, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8985
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:261 original size:96 final size:97
Alignment explanation
Indices: 89--471 Score: 393
Period size: 98 Copynumber: 3.9 Consensus size: 97
79 TTTCACTCGC
* * *
89 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTATACC--CATTTTTCCCAAAACGCC
1 TTTTCCCAAAATGCCTTTCCCGGACGGAAGGCACTTATTTTTACCTGC-TTTTTCCCAAAACGCC
* * *
152 CTTCTCGGACGGAAGGCGTTTATTTTTACCTGT
65 CTTCCCGGACGGAAGGCGCTTATTTTTACCTAT
* * *
185 TTTTCCCAAAGTGCCTTTCCCGGACGGAAGGCACTGATTTTTACCTGC-TTTTCCCAAAATGCCC
1 TTTTCCCAAAATGCCTTTCCCGGACGGAAGGCACTTATTTTTACCTGCTTTTTCCCAAAACGCCC
* *
249 TTCCCGGGCGGAAGGCACTTA-TTTTACTTGCTAT
66 TTCCCGGACGGAAGGCGCTTATTTTTAC---CTAT
* * * * * *
283 TTCTTCCAAAAATG-CTCTTCCCGGACGGAAGACATTTA-TTTTACTTGCTTTTTTCCAAAAATG
1 TT-TTCCCAAAATGCCT-TTCCCGGACGGAAGGCACTTATTTTTACCTGC-TTTTTCCCAAAACG
* *
346 CCCTTCCCGGACGGAAGACGCTTATTTTTACCCACT
63 CCCTTCCCGGACGGAAGGCGCTTATTTTTACCTA-T
* * * * * **
382 TTTTCCCAAAGTGCCTTTCCCGGACGGAATGCACTAACTTTTACTTGCTTTTTCTTAAAACGCCC
1 TTTTCCCAAAATGCCTTTCCCGGACGGAAGGCACTTATTTTTACCTGCTTTTTCCCAAAACGCCC
* *
447 GTCCCGGACGGAAGGCG-TTAATTTT
66 TTCCCGGACGGAAGGCGCTTATTTTT
472 GCTCGCTTTT
Statistics
Matches: 240, Mismatches: 34, Indels: 25
0.80 0.11 0.08
Matches are distributed among these distances:
95 6 0.03
96 72 0.30
97 7 0.03
98 74 0.31
99 42 0.17
100 33 0.14
101 6 0.03
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (97 bp):
TTTTCCCAAAATGCCTTTCCCGGACGGAAGGCACTTATTTTTACCTGCTTTTTCCCAAAACGCCC
TTCCCGGACGGAAGGCGCTTATTTTTACCTAT
Found at i:357 original size:49 final size:49
Alignment explanation
Indices: 89--462 Score: 382
Period size: 48 Copynumber: 7.7 Consensus size: 49
79 TTTCACTCGC
* *
89 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTATACC--CAT
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGC-T
* * **
137 TTTTCCCAAAACGCCCTTCTCGGACGGAAGGCGTTTATTTTTACCTG-T
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCT
* * *
185 TTTTCCCAAAGTGCCTTTCCCGGACGGAAGGCACTGATTTTTACCTGC-
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCT
* *
233 TTTTCCCAAAATGCCCTTCCCGGGCGGAAGGCACTTA-TTTTACTTGCTAT
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGC--T
* * * * *
283 TTCTTCCAAAAATGCTCTTCCCGGACGGAAGACATTTA-TTTTACTTGCTT
1 TT-TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGC-T
* * * **
333 TTTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTATTTTTACCCACT
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCT
* * * * * *
382 TTTTCCCAAAGTGCCTTTCCCGGACGGAATGCACTAACTTTTACTTGCT
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCT
** * *
431 TTTTCTTAAAACGCCCGTCCCGGACGGAAGGC
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGC
463 GTTAATTTTG
Statistics
Matches: 272, Mismatches: 46, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
47 9 0.03
48 115 0.42
49 96 0.35
50 12 0.04
51 40 0.15
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (49 bp):
TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGCT
Found at i:1105 original size:22 final size:23
Alignment explanation
Indices: 1080--1124 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1070 GTGATGAACA
* *
1080 AGAGAAAAT-GGCGCGGAGCTTG
1 AGAGAAAATAAGCACGGAGCTTG
1102 AGAGAAAATAAGCACGGAGCTTG
1 AGAGAAAATAAGCACGGAGCTTG
1125 GGTTTTTGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.38, C:0.13, G:0.36, T:0.13
Consensus pattern (23 bp):
AGAGAAAATAAGCACGGAGCTTG
Found at i:1444 original size:17 final size:17
Alignment explanation
Indices: 1422--1454 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1412 TCCCAGTCAT
1422 GGTACCAGGTAGCATGA
1 GGTACCAGGTAGCATGA
1439 GGTACCAGGTAGCATG
1 GGTACCAGGTAGCATG
1455 TGTTGTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (17 bp):
GGTACCAGGTAGCATGA
Found at i:2314 original size:156 final size:156
Alignment explanation
Indices: 1782--2322 Score: 596
Period size: 156 Copynumber: 3.5 Consensus size: 156
1772 TGGTGAACTA
*
1782 GGTTTCACACCTCAAATTGTACTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAAT
1 GGTTTCACACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAAT
* * * * *
1847 GAGTTGAAACTTTGCCA-AGGGACTTAGATTCTCTCCACAAGACTATGGACAAAATTCTAAGTAA
66 GAGATGAAACTTTGCCACAGAGACTTAGATTATCTCCATAAGA-TATGGAAAAAATTCTAAGTAA
* * * * * *
1911 AACCGAGCTCCCCTTG-ATGGTGAACTA
130 AACCGAACT-CCCTAGCATAGAGAAGTT
* * ** * *
1938 GGTTTCTCTCC-CAGGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTCCATTCTAAGT-TCAAT
1 GGTTTCACACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAAT
* * * *
2001 GAAGTTG--A-TTTTCCACTAGTAGACTTAGATTATCCCCATAAAGATATGGGAAAAATTCTAAG
66 G-AGATGAAACTTTGCCAC-AG-AGACTTAGATTATCTCCAT-AAGATATGGAAAAAATTCTAAG
* *
2063 TAAAACCGACCTCTCTAGCATAGAGAAGTT
127 TAAAACCGAACTCCCTAGCATAGAGAAGTT
* * **
2093 GGTTTCACACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCA-TCTTAAGCCCGTT
1 GGTTTCACACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTC-TAAGTCTGAA
* * *
2157 TGAGATGAAACTTGGCCACA-AGACTTAGAATATCTCCATAAGATGATGGAAAAAACTCTAAGTA
65 TGAGATGAAACTTTGCCACAGAGACTTAGATTATCTCCATAAGAT-ATGGAAAAAATTCTAAGTA
* *
2221 AAACTGAACTCCCTAGCATAAAGAAGTT
129 AAACCGAACTCCCTAGCATAGAGAAGTT
* * * * **
2249 GGTTTCACACCTCAAATTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCATACGAAGTCTGTTT
1 GGTTTCACACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAAT
2314 GAGATGAAA
66 GAGATGAAA
2323 TTTCACCAAG
Statistics
Matches: 323, Mismatches: 48, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
152 6 0.02
153 1 0.00
154 11 0.03
155 113 0.35
156 181 0.56
157 3 0.01
158 2 0.01
159 6 0.02
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (156 bp):
GGTTTCACACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAAT
GAGATGAAACTTTGCCACAGAGACTTAGATTATCTCCATAAGATATGGAAAAAATTCTAAGTAAA
ACCGAACTCCCTAGCATAGAGAAGTT
Found at i:2367 original size:156 final size:155
Alignment explanation
Indices: 2049--2368 Score: 385
Period size: 156 Copynumber: 2.1 Consensus size: 155
2039 TAAAGATATG
* * * *
2049 GGAAAAATTCTAAGTAAAACCGACCTCTCTAGCATAGAGAAGTTGGTTTCACACCTCAAATTGTC
1 GGAAAAACTCTAAGTAAAACCGAACTCCCTAGCATAAAGAAGTTGGTTTCACACCTCAAATTGTC
* **
2114 CTTAAATGAAAAACTAGCATAAGTTTTTCATCTTAAGCCCGTTTGAGATGAAACTTGGCCACAAG
66 CTTAAATGAAAAACTAGCATAAGTTTTTCATCTGAAGCCCGTTTGAGATGAAACTTCACCACAAG
* * * * * *
2179 ACTTAGAATATCTCCATAAGATGAT
131 ACCTAGAATATATCAAGAACATCAT
*
2204 GGAAAAAACTCTAAGTAAAACTGAACTCCCTAGCATAAAGAAGTTGGTTTCACACCTCAAATTGT
1 GG-AAAAACTCTAAGTAAAACCGAACTCCCTAGCATAAAGAAGTTGGTTTCACACCTCAAATTGT
* * * * *
2269 CCTTAACTGAAAAACTTGCATAAGTTTTTCATAC-GAAGTCTGTTTGAGATGAAATTTCACCA-A
65 CCTTAAATGAAAAACTAGCATAAGTTTTTCAT-CTGAAGCCCGTTTGAGATGAAACTTCACCACA
* *
2332 GATGACCTA-CATGTATCAAGGAACATCAT
129 -A-GACCTAGAATATATCAA-GAACATCAT
2361 GGAAAAAC
1 GGAAAAAC
2369 CCCCTATCAA
Statistics
Matches: 139, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
155 3 0.02
156 122 0.88
157 14 0.10
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (155 bp):
GGAAAAACTCTAAGTAAAACCGAACTCCCTAGCATAAAGAAGTTGGTTTCACACCTCAAATTGTC
CTTAAATGAAAAACTAGCATAAGTTTTTCATCTGAAGCCCGTTTGAGATGAAACTTCACCACAAG
ACCTAGAATATATCAAGAACATCAT
Found at i:3312 original size:25 final size:29
Alignment explanation
Indices: 3258--3313 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 29
3248 TTTCTTCTAA
3258 TCTTCTAAATTCTGTCTTGACTTGAGTAT
1 TCTTCTAAATTCTGTCTTGACTTGAGTAT
*
3287 TCTTC-AAA-TCTG-CTTG-CTTGATTAT
1 TCTTCTAAATTCTGTCTTGACTTGAGTAT
3312 TC
1 TC
3314 AGCTGTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 10 0.38
26 4 0.15
27 4 0.15
28 3 0.12
29 5 0.19
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (29 bp):
TCTTCTAAATTCTGTCTTGACTTGAGTAT
Found at i:5264 original size:24 final size:24
Alignment explanation
Indices: 5236--5281 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5226 GGGCGGCAAG
5236 GCTATTTTTTTAAAAAAAAAATTA
1 GCTATTTTTTTAAAAAAAAAATTA
*
5260 GCTATTTTTTTAAAAAAGAAAT
1 GCTATTTTTTTAAAAAAAAAAT
5282 GGGTTTAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (24 bp):
GCTATTTTTTTAAAAAAAAAATTA
Found at i:5927 original size:22 final size:22
Alignment explanation
Indices: 5902--5951 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
5892 CCAACTTAAA
* *
5902 TATTTTTTATAAAATATAATTT
1 TATTTTCTACAAAATATAATTT
5924 TATTTTCTACAAAATATAATTT
1 TATTTTCTACAAAATATAATTT
*
5946 CATTTT
1 TATTTT
5952 AAAAATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTTTCTACAAAATATAATTT
Found at i:6977 original size:22 final size:22
Alignment explanation
Indices: 6883--7241 Score: 261
Period size: 22 Copynumber: 16.4 Consensus size: 22
6873 ACTTTGCAGA
*
6883 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
** * * *
6905 CCACCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAGTGAGG
*
6927 TTA-CAAAAATTTCATCGAT-A-G
1 TTATC-AAAATTTCATAG-TGAGG
* *
6948 TAATCAAAATTTCATAGTGAGA
1 TTATCAAAATTTCATAGTGAGG
* * * *
6970 TTAACAAAA-TTCTGTAGGGAAG
1 TTATCAAAATTTC-ATAGTGAGG
* * *
6992 TGATCAACA-TTCTATAGGGAGG
1 TTATCAAAATTTC-ATAGTGAGG
7014 TTATCAAAATTTCATTACGT--GG
1 TTATCAAAATTTCA-TA-GTGAGG
* *
7036 TTATCAAAATTTTATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
7058 TTATTAAAATTACATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
*
7080 TTATCAAAGTTTCATA-TGAGG
1 TTATCAAAATTTCATAGTGAGG
*
7101 TTATCAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
7123 CTACCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAGTGAGG
* * *
7145 TTATTAAAATTTCATAGGGTGG
1 TTATCAAAATTTCATAGTGAGG
7167 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
7189 TTA-CTAAAATTACATTGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
7211 TTACCAAAACTTCATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
7233 TTATCAAAA
1 TTATCAAAA
7242 GCACTTGTAG
Statistics
Matches: 266, Mismatches: 56, Indels: 30
0.76 0.16 0.09
Matches are distributed among these distances:
20 2 0.01
21 41 0.15
22 215 0.81
23 7 0.03
24 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:7113 original size:87 final size:88
Alignment explanation
Indices: 7005--7265 Score: 265
Period size: 87 Copynumber: 3.0 Consensus size: 88
6995 TCAACATTCT
* * * * * *
7005 ATAGGGAGGTTATCAAAATTTCATTACGTGGTTATCAAAATTTTATAGCGAGGTTATTAAAATTA
1 ATAGTGAGGTTATCAAAATTTCATTACGAGGCTACCAAAATTTCATAACGAGGTTATTAAAATTA
*
7070 CATAGGGAGGTTATCAAAGTTTC
66 CATAGGGAGGTTATCAAAATTTC
* * * * *
7093 ATA-TGAGGTTATCAAAATTTCATAATGAGGCTACCAAAATTTCATAATGTGGTTATTAAAATTT
1 ATAGTGAGGTTATCAAAATTTCATTACGAGGCTACCAAAATTTCATAACGAGGTTATTAAAATTA
*
7157 CATAGGGTGGTTATCAAAATTTC
66 CATAGGGAGGTTATCAAAATTTC
* ** * * ** * **
7180 ATAGTGAGGTTA-CTAAAATTACATTGGGAGGTTACCAAAACTTCATATGGAGGTTATCAAAAGC
1 ATAGTGAGGTTATC-AAAATTTCATTACGAGGCTACCAAAATTTCATAACGAGGTTATTAAAATT
*
7244 ACTTGTAGGGAGGTTATCAAAA
65 AC--ATAGGGAGGTTATCAAAA
7266 GTAGTATTTC
Statistics
Matches: 141, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
87 75 0.53
88 50 0.35
90 16 0.11
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.33
Consensus pattern (88 bp):
ATAGTGAGGTTATCAAAATTTCATTACGAGGCTACCAAAATTTCATAACGAGGTTATTAAAATTA
CATAGGGAGGTTATCAAAATTTC
Found at i:7749 original size:2 final size:2
Alignment explanation
Indices: 7736--7773 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
7726 GTCAGATAAC
*
7736 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7774 AACATAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.